An evolutionary dilemma!!!!

It's not your place to comment on science. You're not a scientist. You're a fraud.
Your opinion is meaningless and ill-conceived. In short, you don't count.

End of message.

But I'm accused of trolling for telling the truth about what's being done on this forum on a regular basis...

Discredit anyone questioning evolutionary philosophies; including the use of painting a picture that I described earlier, both for self-confirmation
and expressing that picture+pride+arrogance/a haughty spirit, looking down your nose at those who disagree with you or refuse to accept your picture
of both yourself and the one you disagree with, i.e. expressing your intellectual superiority complex. No offence intended, just calling it as I see
it, no blame either. Also having an effect on others by expressing those pictures and views of both yourself and others that disagree with you or
those who think like you do about these subjects. Hope it gets people's minds of the subjects that are raised. Play your other cards in your house of
cards (someone else with the Lenski stuff). And accuse anyone who points this out of doing similar things themselves and posting off-topic (or in the
wrong thread apparently). Or pretending you've got no idea what they're talking about (or 1 step further, implying it's gibberish, ridiculing the
subject or points brought up regarding their own behaviour as if its not worthy of anyone's attention cause it's just gibberish, trolling, ranting,
rhetoric, psychological projection, etc. More psychological projection of their own).

And don't forget the ever so popular appeal to 'The Great We Don't Know Yet (but Mother Nature did it anyway), work is in progress'-God of the
agnostic gaps and philosophy of vagueness/uncertainty to brush the contradicting evidence under the carpet with the main excuse: 'we don't know all
the details yet', when the relevant details are well established and demonstrating the earlier claim to be without proper logical supporting evidence
but with contradicting evidence and major flaws in the storyline (wish I could share a video here of the character Lucius Lavin in the Stargate
Atlantis show explaining the flaws away in his story to Sheppard after he starts asking tricky questions about his story, very reminiscent of certain
behaviour again). The part and main unsupported (by proper honest untwisted evidence) claim that 'Nature did it' often not spelled out. The main
pillar of philosophical naturalism posing as "science", which in turn is the main pillar for evolutionary philosophies (and the general claim 'Nature
did it' that is often hidden behind the verb "evolve" or other ways to express that notion regarding the original cause of specific phenomena).

Can't be reasonable with the unreasonable (unless you can change that behaviour, a worthy goal that I have gotten into on other occasions, but very
tricky to accomplish):

Proverbs 29:9:

When a wise man enters into a controversy with a fool, There will be ranting and ridicule, but no satisfaction.

there is no evolutionary dilemma. you were confused by a few papers on the internet and decided evolution is inaccurate because your understanding is
inaccurate. your agenda is a) disprove evolution and b) make science look unreliable as a secular methodology, which gives us c) all hail god and
creationism as the superior theory. but you know, its whatever.

If you're not intentionally lying then you have some mental block preventing you from understanding basic biology. Why don't face the fact that you're
no good at this. Novel phenotypes are gains in function.

You don't seem to understand that their are two perspectives when it comes to looking at a mutation. It may appear as a gain in function from the
perspective of the phenotype, but the molecule perspective is the one that ultimately tells us what kind of mutation it was. I've given sources on
this already. Its not that I don't understand its that you cannot even think of questioning evolution. It's about as bad as trying to discuss
Christianity with a Mormon.

Are you suggesting that Craig Venter could just have looked up Google Scholar?

The point is that, despite glib responses regarding codon reassignment, there is some degree of validity to the suggestion that there isn't a single
phylogenetic tree.

Even W. Ford Doolittle, the 'inventor' of the HGT paradigm, has published articles such as "Uprooting the Tree of Life" and has suggested that he no
longer believes in a single universal common ancestor. He specifically talks about how Archaeoglobus fulgidus is anomalous to the developmental
sequence proposed by the phylogenetic tree and his concept now is that life developed from colonies of similar primitive organisms that shared code.

resist all you want, but posting poorly formulated attacks on a conspiracy forum is probably not the most effective approach.

....oh the irony...

So at which point do you reckon a certain kind of people can quit it with the ad hominem-game and get back to addressing anything detailed about the
subject that was raised rather than talking about the person who raised it? (other than, oh it's no issue, not interesting, another topic
please...along with the 'you just don't understand' and 'you're not a scientist' commentary and fancy storytelling and inventing new parts to the
story or adding new storylines á la Lucius Lavin answering questions)?

As long as it works so well...I'm not keeping my hopes up.

Propaganda....it works, bi...you lovers of knowledge that have forgotten* to use their thinking abilities properly and healthily and are capable of so
much more than this. (*: not exclusively by their own doing but by bad associations and conditioning with propaganda, while projecting that on those
who have been trying to warn you and explain in more detail how it works and how one is affected, as well as the contagious nature of it)

resist all you want, but posting poorly formulated attacks on a conspiracy forum is probably not the most effective approach.

....oh the irony...

So at which point do you reckon a certain kind of people can quit it with the ad hominem-game and get back to addressing anything detailed about the
subject that was raised rather than talking about the person who raised it? (other than, oh it's no issue, not interesting, another topic
please...along with the 'you just don't understand' and 'you're not a scientist' commentary)?

As long as it works so well...I'm not keeping my hopes up.

Propaganda....it works, bi...you lovers of knowledge that have forgotten* to use their thinking abilities properly and healthily and are capable of so
much more than this. (*: not exclusively by their own doing but by bad associations and conditioning with propaganda, while projecting that on those
who have been trying to warn you and explain in more detail how it works and how one is affected, as well as the contagious nature of it)

in that case, I welcome you to propose an alternative hypothesis that may be tested for veracity. if modern evolutionary synthesis is not adequate, by
all means share your superior solution. show us all a better way to look at this puzzle and resolve it.

Probably should have pointed out that he still used 3 different languages in his example. You might also want to consider how different alphabets
(like ancient Hebrew, Chinese) are like different programming languages (or codes).

I see the myth of endosymbiosis* is also still going strong in this thread in spite of a total lack of (proper, reasonable) evidence...(*: note that
there is also a more general use of the term endosymbiosis that I'm not referring to, see below what I'm referring to specifically as the mythology
surrounding it, so not the general definition that shows up if you google it, some people like to conflate fact with fiction by being vague about
details and differences between concepts and notions, see where the bolded parts below for example differ from the general definition; some people
also like others to ignore or overlook the logical requirements for their storyline that can also be found in between the bolded parts)

What do many scientists claim? All living cells fall into two major categories—those with a nucleus and those without. Human, animal, and plant
cells have a nucleus. Bacterial cells do not. Cells with a nucleus are called eukaryotic. Those without a nucleus are known as prokaryotic. Since
prokaryotic cells are relatively less complex than eukaryotic cells, many believe that animal and plant cells must have evolved from bacterial cells.
In fact, many teach that for millions of years, some “simple” prokaryotic cells swallowed other cells but did not digest them. Instead, the theory
goes, unintelligent “nature” figured out a way not only to make radical changes in the function of the ingested cells but also to keep
the adapted cells inside of the “host” cell when it replicated.9*

*: No experimental evidence exists to show that such an event is possible.

What qualifies a theory as a scientific theory? According to the Encyclopedia of Scientific Principles, Laws, and Theories, a scientific
theory, such as Albert Einstein’s theory of gravity, must

- Be observable

- Be reproducible by controlled experiments

- Make accurate predictions

The same encyclopedia defines a hypothesis as “a more tentative observation of facts [than a theory],” yet lends itself “to deductions that
can be experimentally tested.”

For those telling stories about these events for which "No experimental
evidence exists to show that such an event is possible." Please propose a test or present the results of an experiment with which to confirm the
so-called "endosymbiont hypothesis" with certainty/conclusiveness. Let's start with the question whether or not it's even possible (an experiment
showing this event in the manner it is described, see the bolded part about retention after or during replication, will do nicely) let alone whether
or not it did actually happen that way.

Then we can get to discussing whether or not this story should be invoked as an explanation to plug the logical gaps in the overarching evolutionary
philosophies in a variety of places (or as an answer to a variety of questions or issues including now the issues that were brought up in this
thread).

Fancy elaborate storytelling is not "science", "scientific" or following "the scientific method" or proposing a hypothesis. Nor is appealing to them a
logical justification to pretend something isn't a probem for the philosophies you are defending and promoting (cause no facts are a problem for your
beliefs in these false stories/myths anyway, and demonstrating that in the process, don't let the facts stop you from telling stories about
"Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes", sounds really fancy and beguiling, as if they know what
they're talking about. I'll bet you the writers of that article also know that "No experimental evidence exists to show that such an event is
possible." But they leave that inconvenient detail out of their article or obscure it behind elaborate technical jargon using the word "indicates" a
lot whenever conflating facts with fiction while adhering to the 'publish or perish'-mantra sometimes disguised* as a description of a problem in the
so-called "scientific community", I'd call it marketplace or market. Where you have to market your stories and cater to the wishes of the audience,
not much different from Hollywood, and the product isn't much better as a result).

*: I mean it's used as a mantra or it functions as a mantra, not that the description that it's a problem or issue is wrong, but I've had someone
point out to me that it's not a mantra but a problem that is being (or has been) discussed under that phrase, but that doesn't take away that whenever
the phrase is heard by a scientist that is trying to be succesful in his career, that it doesn't function as a mantra. So it's both a problem and a
mantra, you can't disguise it's a mantra by pointing out it's a problem. Just to be clear, from wikipedia on the subject:

"Publish or perish" is a phrase coined to describe the pressure in academia to rapidly and continually publish academic work to sustain or further
one's career.
...[whereislogic: now for a description of what I described as "a problem in the so-called scientific community"]
The pressure to publish has been cited as a cause of poor work being submitted to academic journals.
...
This phenomenon has been strongly criticized, the most notable grounds being that the emphasis on publishing may decrease the value of resulting
scholarship, as scholars must spend more time scrambling to publish whatever they can get into print, rather than spending time developing significant
research agendas.[11] Similarly, humanities scholar Camille Paglia has described the publish or perish paradigm as "tyranny" and further writes that
"The [academic] profession has become obsessed with quantity rather than quality. [...] One brilliant article should outweigh one mediocre book."
...
Also, publish-or-perish is linked to scientific misconduct or at least questionable ethics.
...

And so on...obviously no mention of how conducive it is to selling false stories/myths, vague falsehoods and fiction as "science" and "hypotheses",
they prefer talking about "scientific misconduct" and "at least questionable ethics".

Genetecist Craig Venter (of the Human Genome Project among other things) in a science forum at Arizona State University, in April 2011, with
other scientists discussing evolution, made the comment that there was not likely to be a single tree of life, but rather - many bushes.

Other panelists - like the journalist and writer Richard Dawkins, suggested that Venter, the preeminent genetecist in the world, was wrong, primarily
because they hold to the paradigm of a single "tree of life".

The truth is at the link. As usual, you receive the benefit of the doubt as to your motives, although it is remarkable how many Creationist lies you
have posted, implying them to be true, in your career at ATS.

a reply to: whereislogic
I often like the way this man describes the behaviour in relation to the subjects I discussed regarding people with a particular way of thinking and
doing things including the stuff I said about 'publish or perish'. Check out for example what he says after 9 minutes (ignore what's said at 12:55, I
have strong doubts that information is entirely accurate, you can continue at 13:08, the main stuff I'm referring to starts at 15:20; I'd change the
question and response at 18:37 but I won't go into how I'd change it now unless someone else wants to give some proposals first to show they've given
it some thought. I'd also like to add "the so-called endosymbiont hypothesis" to Stephen Meyer's examples ending at 20:08; there's no point in
listening to the promotion of his personal agnosticism after 23:49 and attributing it to others when he uses "we" at 25:55.):

Regarding my earlier sidenote:

(*: note that there is also a more general use of the term endosymbiosis that I'm not referring to, see below what I'm referring to
specifically as the mythology surrounding it, so not the general definition that shows up if you google it, some people like to conflate fact with
fiction by being vague about details and differences between concepts and notions, see where the bolded parts below for example differ from the
general definition; some people also like others to ignore or overlook the logical requirements for their storyline that can also be found in between
the bolded parts)

Which is what is done in the conclusion section that Phantom423 quoted from the article he used, using that more general use or definition for the
word "endosymbiosis" to conflate with the logical requirements in the storyline (pretend they're met with that general definition, as if observing an
organism living in another organism is the same thing, it's enough or sufficient evidence for the storyline that involves the part that says or
logically* implies that "unintelligent “nature” figured out a way not only to make radical changes in the function of the ingested cells but also
to keep the adapted cells inside of the “host” cell when it replicated." (*: logically in the sense of following through the logic of the
storyline, not that the storyline in its entirety is logical, if you make a claim, it has logical requirements and implications) And the rest of the
storyline that I skipped now. Caveat: the article that Phantom423 used actually defined "endosymbiosis" as: "one cell living within another" whereas
the google dictionary says "organism" instead of "cell", keeping it nicely vague and confusing and making no mention of the aspects of the story I was
zooming in on.

I could use the last part of Phantom423's comment with some slight adjustments and apply it appropiately to the source article he used (unlike others
who prefer to use psychological projection or are trained by others with viewing it that way, or perhaps better described as 'pot calling the kettle
black' then):

Your source pulled a conclusion out of a hat and just like magic, it looked good, therefore, it worked - who would ever challenge such an
innovative conclusion?!! No objective analysis, [irrelevant] lab work, [laughably biased] corroborating references [that are based on the same
methodology of making stuff up without proper evidence or even an attempt to prove the claims conclusively, only supported by twisting and
cherry-picking facts to paint a picture of what 'may be', or support it, and then sometimes even talking about it as if it's already confirmed to 'be
so'] - just a few pages of unreliable [sophistry laced with beguiling technical jargon] with no [proper, reasonable] evidence [, untwisted, not
misrepresented or leaving out inconvenient facts that show otherwise or something else, or why the proposed or so-called "evidence" doesn't work
logically or reasonably]. The usual scenario which suits their agenda.

Regarding the subject of using a more general definition or explanation for the topic of "endosymbiosis" as opposed to a more complete version of the
storyline as it applies to the philosophy or myth of endosymbiosis (the part for which "no experimental evidence exists to show that such an event is
possible", as earlier described before that quotation, which is also just a short description); it's similar to the way the word "evolution" and all
its different meanings and usages are obscured and where myths are conflated with facts (common ancestry of all living organisms is the myth, that
organisms change over time is a fact, what's important is how they change over time, which doesn't show common ancestry of all living
organisms).

a reply to: whereislogic
or that natural processes are the exclusive cause for all the varieties of lifeforms (wherever found, whether that be in the DNA or the endresult,
a.k.a. the phenotype), i.e. Nature didn't do it alone. I agree with Newton's argument of induction (and conclusion) that should not be evaded by
hypotheses (and certainly not myths that don't even qualify as proper hypotheses): it would have been a mess otherwise (see his reasoning at 3:22) or
better said it would not have resulted in viable healthy organisms capable of surviving and reproducing in a variety of environments as they do now
(with such a low neglectable number of defects in reproduction that entire groups and kinds of organisms can continue to thrive):

I agree with you. Life could have started multiple times. But the complexity of the topic is so deep that discussing it here on ATS without a set of
references that cover the entire subject, makes it a useless endeavor. Just my opinion.

The OP has no working knowledge of science. Probably has never been in a lab, doesn't understand how the scientific method works - on and on. In
other words, anyone who responds to the OP, is obliged to begin with the basics.

I'm not a molecular biologist. I'm a biochemist and my specialty is spectroscopy. I have a Ph.D. in biochemistry and biophysics. I don't mind
diving into a topic as long as others make an equal contribution. So if you want to start a serious thread about the tree of life and questions
surrounding it, I'm happy to participate. But every time someone starts a serious thread, it devolves into a food fight defending one's self against
the fraud and deception of Creationism.

So up to you. If you want to discuss the topic, happy to do so. It's very interesting and everyone can learn something by doing the research.

In science, no question is verboten. Without good questions, answers would never be found and knowledge would never move forward.

That said, you claim to "tell the truth". Well science isn't about truth. Science is about discovery and evidence. That's it. If you discover
something, you're required to provide the evidence. The evidence can be challenged by anyone who understands the subject.

You write pages of opinion but never present hard evidence. Think of it this way: if I'm working on developing a new drug for cancer, I must present
statistical evidence that it works. Then others in the field will challenge my discovery and repeat the experiment including clinical trials. If
they find a flaw in my evidence or the clinical trials don't work out, then it's up to me to acknowledge that there's a flaw somewhere and try to find
it. When you guys post your "evidence", all you do is write up an opinion citing crackpots from Creationist websites. I'm sorry for you, but that
ain't science and never will be.

You want to discuss a topic in science, at the very least you need to be able to discuss it with a scientist in a coherent, credible way. Otherwise,
it's a waste of time.

The problem is different alphabets aren't like different programming languages, which is why I told him it was a bad analogy for what I am talking
about. Yes each language and programming language has rules of syntax, but in general for regular language we use different patterns of sounds to
deliver the same information, so one could say a sentence in english or spanish(different codons) and understand the same message(produce the same
amino acid or process). However in the context of programming languages if you try and write certain JAVA commands(some particular codon or
arrangement of codons from say a Mycoplasma) in a C# environment(in Human cell environment) it will simply break. You just can't do it.

a reply to: Phantom423
Fact regarding the so-called "endosymbiont hypothesis" (not a proper hypothesis as I explained) that was used in the article you used and treated as
if it's already established to have happened (multiple times):

"No experimental evidence exists to show that such an event is possible".

This is not an opinion but (in combination with how you and the article you used use this story) hard evidence of what wikipedia would call
"scientific misconduct" or "questionable ethics" and I would call fancy storytelling presented as "science".

If there was no endosymbiosis in the manner it is described earlier before the fact mentioned above about "no experimental evidence..." there also is
no "endosymbiotic gene transfer from prokaryotic pangenomes". Anyway, it's not up to me to provide evidence regarding the topic of endosymbiosis as
it's used in the myth of endosymbiosis regarding prokaryotic organisms (again as described earlier). I didn't introduce the topic to the thread or by
doing that make reasonable and alert people aware that mythology is published as "science", and then used by the fans of evolutionary philosophies as
so-called evidence or explanations.

Why did no one during the so-called "peer review" mention any objection to the obvious flaw in the research you used that the whole analysis is based
on a myth for which "No experimental evidence exists to show that such an event is possible" making their research invalid and irrelevant, pure
imagination, erronuous assumptions built on erronuous assumptions and wishful thinking? And to sell (by support, by rolling with it, by treating the
story as if it's science or scientific) yet another made up story about how prokaryotic organisms gave rise to eukaryotic organisms? Whatever happened
to proper peer review? What happened to extraordinary claims require extraordinary evidence?

I'd be happy with just 1 piece of proper evidence, doesn't have to be extraordinary, just don't use the conflation trick (also used in combination
with fallacies of equivocation or 'bait and switch': the listener is baited on one meaning of a word, and then the meaning is switched to draw a
faulty conclusion. This also happens with stripping down the meaning to not refer to details that are important to consider in relation to the story
or claims attached to the word, as I tried to explain in more detail before using the terminology "general definition", stripped down of those
details, opening up the option of pointing to something that does qualify under the general definition but doesn't fulfill those details in the
storyline), cause that's hard evidence for something else again. I'd like to see an experiment in which the claimed event happens as it is claimed in
its enitrety, with the important details that I mentioned in my commentary earlier, the logical requirements for the story that are completely ignored
in the article you used. So start experimenting on those prokaryotic organisms. 'Put up or shut up' is the saying I mentioned weeks ago (the last time
I saw someone post a link about the same myth) I'm not entirely comfortable with using because it might sound a bit too harsh, but it is what it boils
down to (before you start linking to articles talking about the myth of endosymbiosis as if it needs no further verification before one can base their
'research' on it, or their fancy storytelling).

The fact that you don't or can't understand studies is not my problem. There are plenty of experiments that show mutations create new alleles. Here
are a few, free of charge!

You are obviously a Neo-darwinist which has been proven to be incorrect in many of its assumptions:

Neo-Darwinian evolution is uniformitarian in that it assumes that all process works the same way, so that evolution of enzymes or flower colors can be
used as current proxies for study of evolution of the body plan. It erroneously assumes that change in protein coding sequence is the basic cause of
change in developmental program; and it erroneously assumes that evolutionary change in body plan morphology occurs by a continuous process. All of
these assumptions are basically counterfactual. This cannot be surprising, since the Neo-Darwinian Synthesis from which these ideas stem was a
pre-molecular biology concoction focused on population genetics and adaptation natural history, neither of which have any direct mechanistic import
for the genomic regulatory systems that drive embryonic development of the body plan...

Therefore the action of selection differs across dGRN structure. Selection does not operate to produce continuous adaptive change except at the dGRN
periphery. The lack of continuous variation in morphogenetic traits defining Class and Phylum level clades is obvious in the striking evolutionary
stasis revealed by the fossil record (Davidson and Erwin, 2006; 2009; Erwin, 2011). In other words, while cis-regulatory sequence variation may have
continuing adaptive significance at the dGRN periphery, at upper levels of the dGRN hierarchy it does not have the same significance because the
system level output is very impervious to change, except for catastrophic loss of the body part or loss of viability altogether.

No one has questioned whether mutation can create new alleles, but changes in the protein coding sequence are not the basic cause of change in the
development program. The paper I've given you is from Eric H. Davidson who specialized in work in the developmental biology. This paper calls for
people to attempt to find a new mechanistic approach to body plan morphogenesis. As you can see when we change the upper levels of the dGRN hierarchy
we do nothing but cause catastrophic loss of body parts or viability all together.

Bacteria/Microbes Here they identified 66 mutations to that one focal gene which had an adaptive, or beneficial, effect on the fitness of
individual

Here they used these results to develop a mathematical model of the probability of a beneficial mutation reaching fixation.

You are confusing the terms beneficial mutation and gain in function mutation. Beneficial mutations are simply mutations which help the organism
survive, it says nothing about whether something was added, modified, or removed at the molecular perspective. A red herring mixed with a strawman you
are doing well! This does nothing to disprove the source I sent to you earlier from Behe. Behe's work came 8 or 10 years after this paper, if it
showed he was wrong I highly doubt it would have made it into the Quarterly Review of Biology. What you don't seem to realize is everything in that
paper is talking about how an organism adapts, but nothing in their research proves that body plan morphogenesis can occur. It just shows that
variation among species occurs, and I've never questioned that. A beneficial mutation does not equate to body plan morphogenesis nor does it eqaute to
a gain in function mutation. A mutation is beneficial or deleterious depending on how it effects the organisms fitness level. A mutation is a gain or
loss of function mutation depends on how it effects protein
function(mcb.berkeley.edu... page 17). Gain and loss can be broken
into subcategories, only one of the categories of a gain in function mutation actually refers to a new function to be given to a protein. According to
Behe's source in 2010, no mutation that caused acquisition of protein function had been identified. Lenksi's E coli was a possibility but I've already
posted a source showing that all the mutation did was allow a protein that was already present to operate in the presence of oxygen. So it was an
increase in function from the molecular perspective. So yes some people classify that as gain in function. Behe's paper referred to an increase in
function as modification of function. So his paper is claiming there have been no mutations observed that are actually the acquisition of a new
protein function.

I have not said beneficial mutations, or mutations that help the fitness of the organism, don't occur. You seem to be under the misconception that I
disagree with absolutely every aspect of the theory. I only disagree with aspects of the theory surrounding the evolution of new morphological
features not dealing with variation among species or natural selection. In order to gain new morphological features you need a mutation to occur at
the high end of the dGRN hierarchy, but currently we know of no mechanism that will allow us to do that because the dGRN is canalized, and extremely
impervious to change. Again this if off topic from the OP and is just you distracting from the real issue at hand but whatever.

Abstract Lipoprotein lipase (LPL) hydrolyzes triglycerides in the circulation and promotes the hepatic uptake of remnant lipoproteins. Since the gene
was cloned in 1989, more than 100 LPL gene mutations have been identified, the majority of which cause loss of enzymatic function. In contrast to
this, the naturally occurring LPLS447X variant is associated with increased lipolytic function and an anti-atherogenic lipid profile and can
therefore be regarded as a gain-of-function mutation.

FINALLY!!! A source that has to do with something I've discussed! Yes it could be classified as gain in function, but in Behe's paper this would have
fallen under the modification of function category. It didn't acquire new function it increased the function of a Lipoprotein lipase. Again this paper
was published in 2006 before Behe's paper. Highly doubt his would have made it through review had this paper actually shown his conclusion to be
false.

All of these sources except the last one have anything to do with what we were talking about so nice strawmen and red herrings. I've burned all the
scarecrows and shot the bird out of the sky what comes next!

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